Agriculture and Agri-Food Canada, Cereal Research Centre, Canada
The stem rust resistance gene SrTmp carried by Triumph 64 confers resistance to Pgt race TTKSK and other members of the Ug99 race group. While some previous studies have mapped resistance postulated to be SrTmp, none used Triumph 64 as a parent. The purpose of this study was to genetically map SrTmp with DNA markers using a DH population from LMPG/Triumph 64 and compare the map position of SrTmp to previously mapped Sr genes. The DH population was tested with Pgt race TTKSK at the seedling stage. A single gene conditioned resistance to TTKSK (n = 144; χ21:1 = 0.44, p = 0.50). SrTmp was mapped to the distal region of chromosome 6DS with SSR markers. The map location of SrTmp was similar to SrCad and Sr42, which likely represent the same gene. In a concurrent study SNP markers were developed to fine-map SrCad. SNP markers were identified and/or developed using a public SNP database (http://www.cerealsdb.uk.net) and sequence information from an Aegilops tauschii genome sequencing project. Further SNP markers were developed by using resistance gene analogs from chromosome 6D to BLAST exome capture sequences from a set of Canadian wheat cultivars followed by searching for unique SNPs found in SrCad carriers. These SNP markers were added to the map of SrTmp. The map positions of SrTmp and SrCad/Sr42 are very similar. While preliminary data show functional differences between SrTmp and SrCad/Sr42, further analysis is needed to determine whether these genes are allelic or closely linked.
The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Australia
Elite barley breeding lines from the Australian Northern Region Barley Breeding Program were evaluated at the seedling and adult growth stages for resistance to leaf rust (LR) caused by Puccinia hordei. F3:5 lines derived from parental germplasm of different geographic origins were screened in the glasshouse and field spanning four years of trials. The 2009 and 2011 breeding populations (BP1 and BP2) comprised 360 lines and were genotyped with 3,244 polymorphic diversity arrays technology (DArT) markers. The 2012 and 2013 breeding populations (BP3 and BP4) comprised 320 lines genotyped with the DArT GBS array (DArTseq), providing 15,400 high quality polymorphic markers. Association mapping (AM) using the DArT/DArT-seq datasets and phenotypic data from 15 independent LR response assays identified a number of genomic regions associated with resistance. The BP1 and BP2 study detected a total of 15 QTL; 5 QTL co-located with catalogued LR resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, and Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. Markers in common between the DArT and DArTseq datasets enabled integration of mapping results for LR response across the four breeding populations and all QTL detected were visualised on a single map for validation. The adult plant resistance (APR) locus Rph20 was the only region detected in all field environments. Markers and their associated sequences identified in this study will be useful for building QTL combinations involving Rph20, thereby providing stable LR resistance in improved barley cultivars. We will also highlight the advantages of AM using breeding germplasm over traditional bi-parental mapping approaches that underutilise genetic diversity and divert valuable resources into populations of low breeding value.
Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, China
Pathogen migration is a source of new pathogens and pathotypes to a particular region. Studies on origin and migration of pathogens were difficult in the past, but DNA sequence data and new analytical approaches now enable us to analyze population genetic structures from which we can determine possible migration routes. The Himalayan and neighboring regions (Gansu, China) were earlier suggested as putative centers of origin for Puccinia striiformis f. sp. tritici (Pst) and sampling locations for Chinese isolates were strongly focused in South Gansu. Previous field surveys indicated that Yunnan might be the primary source of the Gansu population in China. Using samples collected in 2008 and 2011 we compared the Pst population structures of Yunnan and south Gansu for SNPs in housekeeping genes Cdc2, Ef-1? and Mapk1, and the trajectories of upper air flow during wheat growing seasons from 2005 to 2013. The ancestral haplotype was detected in the Yunnan population, which had higher a mutation rate than the Gansu population, but the latter contained more recombination events. Both populations were highly diverse. There was massive air flow between Yunnan and Gansu with trajectories being mainly from Yunnan to Gansu. We propose a putative dispersal route of Pst from Yunnan to South Gansu, making Yunnan the center of origin for Pst in China, whereas Gansu is a secondary center of origin. It is proposed that Pst migrates from South Asia to Yunnan under the influence of westerly weather patterns, and subsequently spreads to other parts in China. DNA sequence comparisons should be undertaken to compare Pst populations of South Asia and China in order to confirm these hypotheses.
Management of the cereal rusts currently relies on the use of fungicides and varietal resistance. Host resistance can be rapidly overcome by mutations in the pathogen population and for this reason virulence surveys are undertaken worldwide to give early warning on any changes. The UK Cereal Pathogen Virulence Survey (UKCPVS) was established in 1967 following an outbreak of yellow rust on the variety Rothwell Perdix. The UKCPVS currently monitors the wheat yellow rust and brown rust pathogen populations as well as the wheat and barley powdery mildew pathogen populations. A watching brief is maintained on barley yellow rust. In 2011 a new Pst race was detected; named the Warrior race after the variety on which it was first found. Initial tests on differential host lines suggested that the race was another stepwise mutation with an added virulence for Yr7 in addition to a combination of virulences to Yr6, Yr9, Yr17 and Yr32. Other characteristics of this race, however, suggested something different from previous race changes with an increase in telial production seen under field conditions. In addition, this new race was seen simultaneously in multiple locations throughout Europe (www.wheatrust.org) in contrast to the more gradual appearance of new variants seen previously. Subsequent genotypic analysis of isolates (Hubbard et al. 2015, Genome Biol. 16:23) demonstrated that the new race was an exotic incursion. Results presented at the meeting will summarize some of the key changes in the pathogen populations, such as the arrival of the Warrior Pst race in 2011 and the re-emergence of the Glasgow race of the brown rust pathogen in 2014.
Department of Plant Breeding and Biotechnology, University of Eldoret, Kenya
Resistance is the most economically viable approach to curb the threat of rusts in wheat. The defeat of Sr31 and vulnerability of other resistance genes to the highly virulent Pgt race Ug99 and variants led to renewed efforts to discover and deploy resistance genes/QTLs in new durably resistant varieties. Akuri is a CIMMYT-developed bread wheat line exhibiting adult plant resistance (APR) in field trials in Kenya despite susceptibility to many races at the seedling stage. This study was designed to identify genomic regions contributing APR to stem rust in Akuri. One hundred and forty one RILs and parents of an F2:5 Akuri x PBW343 population were evaluated in Njoro for APR to stem rust over three seasons. Composite interval mapping was implemented on Windows QTL Cartographer to detect QTLs at a LOD threshold of 2.5 utilizing 910 high quality SNPs previously typed on the DArT-GBS platform. Preliminary QTL analyses revealed loci on chromosomes 1B, 2B and 3B consistently contributing to stem rust resistance. These QTL respectively explained ~7, 9, and 8% of the phenotypic variation. A comparison with the recently reported QTL consensus map revealed that the QTL herein discovered are probably novel. Work is underway to saturate the identified genomic regions with microsatellite markers to identify candidate, linked markers for use in marker assisted selection (MAS)
National Research Council of Canada, Canada
Plant breeders use naturally occurring resistance genes to fight plant diseases. However, new fungal strains rapidly emerge and defeat these genes. For almost a century, the wheat Lr34 gene has conferred a degree of stable resistance to the wheat rusts, making it one of the most important resistance genes. While sequence homology of the cloned Lr34 gene predicted that it encodes a putative ATP binding cassette (ABC) transporter protein belonging to the ABC G subfamily (also known as Pleiotropic Drug Resistance or PDR), its target transport substrate and mechanism of action remains enigmatic. In an effort to understand this transporter we designed several DNA constructs of the Lr34 gene and expressed them in yeast (Saccharomyces cerevisiae). Here we report the successful expression and purification of functional recombinant Lr34 protein. In vitro proteoliposome translocation assays identified the transport substrate of the Lr34Sus protein and demonstrated that the LR34Res protein has the same transport specificity. We also report the identification of related metabolites from flag leaves of Lr34-expressing wheat plants and discuss the functional relevance of these metabolites to the disease resistance and leaf tip necrosis (LTN) phenotypes caused by expression of Lr34Res.
Department of Economic Development, Jobs, Transport and Resources, Australia
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A whole of industry, co-ordinated system for the assignment of reliable stripe rust, stem rust and leaf rust disease response ratings of current wheat cultivars and advanced breeding lines was developed to meet the needs of the Australian grains industry. Previously there was a lack of national consistency in ratings with each state independently publishing response ratings. However, privatisation of public wheat breeding during the early 2000s, recurrent stripe rust epidemics following a foreign pathotype incursion in 2002, and the dramatic increase in fungicide use provided the impetus to develop a consistent approach to assignment of ratings. Factors that became critical to the process were: 1) access to dedicated rust nurseries in diverse cereal production environments, 2) use of single seed sources for consistent variety identity, 3) control lines that provided consistent rust responses in field nurseries across regions, 4) a centralised repository of current and historical data (provided by the National Variety Trials program), and 5) pathotype identification (provided by the Australian Cereal Rust Control Program (ACRCP)). This system was subsequently documented by the Cereal Pathology Working Group (a sub-committee of the ACRCP consultative committee) and included a dispute resolution process. Currently, with GRDC funding, approximately 200 lines comprising current cultivars and advanced breeding lines, are assessed nationally in dedicated rust nurseries by members of the Working Group. Both current and historical data are reviewed annually by the Working Group with consensus rust responses developed and then scrutinised by wheat breeding companies prior to public release. This whole of industry system has improved timeliness, reliability and consistency of information with ratings used widely by Australian farmers to select cultivars to minimise losses due to rust and to plan appropriate chemical control strategies should resistance be inadequate.
Ambo Plant Protection Research Center, Ethiopia
During the 2014/15 main crop season 831 wheat fields and experimental plots were assessed for diseases; 66.2% were in the Oromiya, 20.3% in Tigray and 13.4% in SNNP regions. The major diseases encountered include rusts, septoria leaf blotches, foot and root diseases, Fusarium head blight and smuts. The overall mean prevalence of stem rust was 61%, yellow rust 22%, leaf rust 18.8% and Septoria leaf blotches 52.9%. The incidence of the important diseases was highest in SNNP region. The mean incidence of yellow rust ranged from 5.7% in Oromiya to 39.2% in SNNP. The lowest incidence of stem rust, 15.9%, was noted in Tigray and the highest, 64.4%, in SNNP. The minimum mean Septoria incidence was 23% in Oromiya, and maximum was 66.7% in SNNP. Stem rust severities varied from 7 MR-MSS in Tigray to 36 MR-MSS in SNNP. Furthermore, the widely grown varieties Digelu and Danda’a were resistant to yellow rust, but susceptible to stem rust. Varieties Meda Wolbu, Hogona and Ogolcho were not affected by any of the rusts in Oromiya. Variety Hidase was susceptible in SNNP. Out of 115 Pgt cultures established from stem rust samples collected from the three regions, races TKTTF, RRTTF, TTKSK, TRTTF and JRCQC were identified. Stem rust samples were collected from varieties Digelu, Danda’a, Kakaba, and Hidase. Race TKTTF, virulent on Digalu and first identified in Oromiya region in 2013, is now present in all areas. Adapted varieties with durable stem rust resistance in Ethiopia remains an urgent requirement.
Crop Diseases Research Institute, Pakistan Agricultural Research Council, Pakistan
Detailed rust surveillance of wheat growing areas in Pakistan was conducted from 2011 to 2014. Information about varietal distribution, growth stage, and rust incidence and severity was collected at 950 locations, and rust samples collected from these locations were subjected to race analysis. Yellow rust showed increasing incidence of high to moderate severity. Commercial cultivars released during 1991 to 2011 showed MS to S reactions. Twenty eight races were identified, most with wide virulence ranges. The frequencies of virulence to Yr1, Yr6, Yr7, Yr8, Yr9, Yr17, Yr27, Yr43, Yr44 and YrExp2 all exceeded 50%. Leaf rust also showed increasing incidence, mainly due to cultivation of the susceptible cv. Sehr-06. Fourteen races were identified. The frequencies of virulence to Lr1, Lr2c, Lr3a, Lr16, Lr26, Lr3c, Lr17a, Lr30, LrB, Lr10, Lr14a, Lr14b and Lr21 exceeded 50%. Virulences to Lr2, Lr9, Lr24, Lr18 and Lr19 were not detected and frequencies of virulence to Lr11 and Lr20 were low. Current and old commercial cultivars showed MS to S reactions. In 2011 and 2014 stem rust incidence was sporadic, but in 2013 it was present at 33 of 232 locations in Sindh, Punjab, Khyber Pakhtunkhwa and Baluchistan. Race RRTTF was identified in all samples.
Horticulture and Crop Science, the Ohio State University, Ohio Agricultural Research and Development Center, USA
Trait and trait stability are important for wheat breeding. Our objectives were to assess the relative efficiency of genomic selection (GS) for various wheat traits and trait stability using four different models. Genotyping was conducted with a 90K SNP chip panel. SNP tagging was used to obtain a subset of 3,919 relatively independent markers for downstream analysis. Phenotyping was conducted on a population consisting of 273 lines, from seven different soft red winter wheat breeding programs in the U.S.A. Eberhart and Russells’ regression and additive main effects and multiplicative interaction (AMMI) models were used to assess trait stability. GS accuracy (r) was assessed for ridge regression best linear unbiased prediction (rr-BLUP), Bayesian ridge regression (BRR), reproducing kernel hilbert space (RKHS), and elastic net (EN). Across all models, GS produced a wide range of accuracies for trait stability (0.1 to 0.65) that varied by trait and stability method. Accuracy was 0.35 for yield and 0.44 for yield stability using AMMI, indicating the viability of GS in selecting lines with both high and stable yield. Our findings lay the foundation for wheat breeding programs in northeastern U.S.A. to implement GS. It also provides useful information for wheat rust researchers: as phenotypic selection for rust resistance can be both expensive and time consuming and rapid evolution of rust pathogens require an emphasis on durable resistance controlled by multiple genes, the GS approach applicable for complex traits thus has potential to achieve higher gains per unit time than traditional breeding for rust resistance.